text: In vivo footprinting is a technique used to analyze the protein-DNA interactions that are occurring in a cell at a given time point.  DNase I can be used as a cleavage agent if the cellular membrane has been permeabilized.  However the most common cleavage agent used is UV irradiation because it penetrates the cell membrane without disrupting cell state and can thus capture interactions that are sensitive to cellular changes.  Once the DNA has been cleaved or damaged by UV, the cells can be lysed and DNA purified for analysis of a region of interest. Ligation-mediated PCR is an alternative method to footprint in vivo.  Once a cleavage agent has been used on the genomic DNA, resulting in single strand breaks, and the DNA is isolated, a linker is added onto the break points.  A region of interest is amplified between the linker and a gene-specific primer, and when run on a polyacrylamide gel, will have a footprint where a protein was bound. In vivo footprinting combined with immunoprecipitation can be used to assess protein specificity at many locations throughout the genome.   The DNA bound to a protein of interest can be immunoprecipitated with an antibody to that protein, and then specific region binding can be assessed using the DNA footprinting technique.